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Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

ABSTRACT: Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

PROVIDER: PRJNA416120 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6230490.fastq.gz	Fastqsanger.gz
	SRR6230500.fastq.gz	Fastqsanger.gz
	SRR6230510.fastq.gz	Fastqsanger.gz
	SRR6230520.fastq.gz	Fastqsanger.gz
	SRR6230481.fastq.gz	Fastqsanger.gz

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Potential role of the CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

Project description:The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes with the CBF pathway being knocked out, we showed the CBF pathway plays a significant role in natural variation of freezing tolerance.

2018-07-30 | GSE106284 | GEO

Potential role of natural variation in the Arabidopsis CBF Pathway contributing to local adaptation of ecotypes collected from Italy and Sweden

Project description:The two Arabidopsis ecotypes that are adapted to Italy and Sweden, respectively, showed different degree of freezing tolerance. By comparing the low temperature transcriptomes of the IT and SW ecotypes, we showed CBF pathway plays a significant role in natural variation of freezing tolerance.

2015-12-30 | GSE67332 | GEO

Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

Project description:Illumina HiSeq RNAseq data from the youngest fully developed leaf collected from two ecotypes of Arabidopsis thaliana, Rodasen-47 (Sweden) and Castelnuovo-12 (Italy), adapted to contrasting local climates, grown at different temperatures and/or light levels. Plants were all vegatively growing in one gallon pots to prevent root bounding. Plants were sampled at the 40th day of growth.

2020-07-14 | GSE154349 | GEO

CBF-dependent and CBF-independent regulatory pathways contribute to the differences in freezing tolerance and cold-regulated gene expression of two Arabidopsis ecotypes locally adapted to sites in Sweden and Italy.

Project description:Arabidopsis thaliana (Arabidopsis) increases in freezing tolerance in response to low nonfreezing temperatures, a phenomenon known as cold acclimation. The CBF regulatory pathway, which contributes to cold acclimation, includes three genes-CBF1, CBF2 and CBF3-encoding closely-related transcription factors that regulate the expression of more than 100 genes-the CBF regulon-that impart freezing tolerance. Here we compare the CBF pathways of two Arabidopsis ecotypes collected from sites in Sweden (SW) and Italy (IT). Previous studies showed that the SW ecotype was more freezing tolerant than the IT ecotype and that the IT ecotype had a nonfunctional CBF2 gene. Here we present results establishing that the difference in CBF2 alleles contributes to the difference in freezing tolerance between the two ecotypes. However, other differences in the CBF pathway as well as CBF-independent pathways contribute the large majority of the difference in freezing tolerance between the two ecotypes. The results also provided evidence that most cold-induced CBF regulon genes in both the SW and IT ecotypes are coregulated by CBF-independent pathways. Additional analysis comparing our results with those published by others examining the Col-0 accession resulted in the identification of 44 CBF regulon genes that were conserved among the three accessions suggesting that they likely have important functions in life at low temperature. The comparison further supported the conclusion that the CBF pathway can account for a large portion of the increase in freezing tolerance that occurs with cold acclimation in a given accession, but that CBF-independent pathways can also make a major contribution.

| S-EPMC6281195 | biostudies-literature

arabidopsis ecotypes-Transcriptionnal response to potyviruses infection in Arabidopsis

Project description:ra06-05_potyvirus-ecotypes - arabidopsis ecotypes - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Four different Arabidopsis ecotypes were inoculated with one Potyviruse. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. RNA fron infected plants was then used for microarrays hybridization. Three biological repeat have been done and two dye-swap. Keywords: normal vs disease comparison

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Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

Project description:Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

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Proteomic comparison of Prochlorococcus marinus ecotypes MED4, MIT9319 and SS120.

Project description:Prochlorococcus marinus is a highly abundant picocyanobacterium in Earth’s oceans and therefore a significant contributor to global primary production. This organism exists as different ecotypes, each occupying particular environments in the euphotic zone that differ in both solar penetration and nutrient levels. The ecotypes analysed here were isolated from depths of 5 m (MED4), 135 m (MIT9313) and 120 m (SS120) and cultured at low illumination. MED4, adapted to high light levels closer to the surface, was compared at both low and high illumination. In contrast to other cyanobacteria such as Synechocystis with a dominance of photosystem I (PSI) over photosystem II (PSII) complexes in the thylakoid membranes, MED4 and MIT9313 showed about equal levels. In MED4, the relative levels were almost the same in both the high and low light cultures. SS120 thylakoids contained a lower cytochrome b6f content and around two-fold more PSII than PSI. Additionally a significantly higher abundance of light-harvesting Pcb proteins was found in SS120 than the other ecotypes. This proteomic comparison was employed in conjunction with thylakoid membrane AFM imaging to rationalize the strategies these ecotypes use to survive in the different oceanic environments.

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Nanostring based analysis of CBF-AML patients

Project description:miR-130a is captured as part of a 798 gene probe set on a microarray plate for 48 CBF patients In the group of patients defined here, survival characteristics and relapse information was collected to unbiasedly assess the impact of any miRNA on survival

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A microenvironment-inspired synthetic 3D model for pancreatic ductal adenocarcinoma organoids - 3D PEG-CBF-0.5 MS

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2021-11-29 | PXD022520 | Pride

A compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes

Project description:Different mechanisms for CBF-MYH11 function in acute myeloid Leukemia (AML) with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of RUNX1 target genes. Here, through genome-wide CBF-MYH11 binding site analysis and quantitative interaction proteomics we found that CBF-MYH11 localizes to RUNX1 occupied promoters where it interacts with TAL1, FLI1 and TBP associated factors (TAFs) in the context of the hematopoietic transcription factors ERG, GATA2 and PU.1/SPI1 and the co regulators EP300 and HDAC1. Transcriptional analysis revealed that upon fusion protein knock down a subset of the CBF-MYH11 target genes show increased expression, confirming a role in transcriptional repression. However, the majority of CBF-MYH11 target genes, including genes implicated in hematopoietic stem cell (HSC) self-renewal such as ID1, LMO1 and JAG1, are actively transcribed and upon fusion protein knock down repressed. Together these results suggest an essential role for CBF-MYH11 in regulating expression of genes involved in maintaining a stem cell phenotype.

2013-09-09 | GSE46044 | GEO

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